NiMo catalysts supported on mesoporous MCM-41 type materials shaped with binder were tested for activity in the hydrodesulfurization of 4,6-dimethyldibenzothiophene (4,6-DMDBT) and the diesel fuel fraction (0.92 wt% of sulfur). The aim of the investigation was to evaluate the effect of ion exchange with protons of Al- or Ti-substituted MCM-41 mesoporous supports. The subjected catalytic systems were NiMo/HAlMCM-41 and NiMo/HTiMCM-41, and for comparison purposes NiMo/AlMCM-41 and NiMo/TiMCM-41. The samples were characterized by N2 sorption (at 77 K), XRD, TEM, XPS, SEM and Py–IR. It was found that the functionalization of AlMCM-41 and TiMCM-41 with protons increased the conversion of 4,6-DMDBT and the pseudo-first-order rate constant. Correspondingly, 4,6-DMDBT HDS reactions over the NiMo/HTiMCM-41 catalyst proceeded to a similar extent via hydrogenation and direct desulfurization, whereas over the NiMo/HAlMCM-41 they proceeded mainly via direct desulfurization. Furthermore, the ion-exchanged catalysts displayed two-fold higher efficiency in direct desulfurization than their non-modified counterparts. The NiMo/HTiMCM-41 catalyst exhibited the highest catalytic efficiency in the HDS of 4,6-DMDBT and the diesel oil fraction. The high activity of the NiMo/HTiMCM-41 catalyst is mainly attributed to its appropriate acidity, as well as the metal–support interaction providing both the high dispersion of the active phase and the desirable multilayered stacking morphology of the active phase slabs.